#################################################################################
# Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright
#   notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
#   notice, this list of conditions and the following disclaimer in the
#   documentation and/or other materials provided with the distribution.
# * Neither the name of Pacific Biosciences nor the names of its
#   contributors may be used to endorse or promote products derived from
#   this software without specific prior written permission.
#
# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
# THIS LICENSE.  THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
# BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
# IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
#################################################################################

# Author: David Alexander

import numpy as np

class UnavailableFeature(Exception): pass
class Unimplemented(Exception):      pass
class ReferenceMismatch(Exception):  pass

PULSE_FEATURE_TAGS = { "InsertionQV"    : ("iq", "qv",   np.uint8),
                       "DeletionQV"     : ("dq", "qv",   np.uint8),
                       "DeletionTag"    : ("dt", "base", np.int8 ),
                       "SubstitutionQV" : ("sq", "qv",   np.uint8),
                       "MergeQV"        : ("mq", "qv",   np.uint8) }

COMPLEMENT_MAP = { "A" : "T",
                   "T" : "A",
                   "C" : "G",
                   "G" : "C",
                   "N" : "N",
                   "-" : "-" }

def complementAscii(a):
    return np.array([ord(COMPLEMENT_MAP[chr(b)]) for b in a], dtype=np.int8)

def reverseComplementAscii(a):
    return complementAscii(a)[::-1]


BAM_CMATCH     = 0
BAM_CINS       = 1
BAM_CDEL       = 2
BAM_CREF_SKIP  = 3
BAM_CSOFT_CLIP = 4
BAM_CHARD_CLIP = 5
BAM_CPAD       = 6
BAM_CEQUAL     = 7
BAM_CDIFF      = 8
